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Drat, forgot the unit tests again

This commit is contained in:
Eric Banks 2012-06-12 19:00:47 -04:00
parent bacd25d1a4
commit bb77aa88c3
3 changed files with 18 additions and 19 deletions
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13
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadCovariatesUnitTest.java
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@ -6,9 +6,6 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.List;
/** /**
* @author carneiro * @author carneiro
* @since 4/21/12 * @since 4/21/12
@ -38,11 +35,11 @@ public class ReadCovariatesUnitTest {
coCov.initialize(RAC); coCov.initialize(RAC);
cyCov.initialize(RAC); cyCov.initialize(RAC);
List<Covariate> requestedCovariates = new ArrayList<Covariate>(4); Covariate[] requestedCovariates = new Covariate[4];
requestedCovariates.add(rgCov); requestedCovariates[0] = rgCov;
requestedCovariates.add(qsCov); requestedCovariates[1] = qsCov;
requestedCovariates.add(coCov); requestedCovariates[2] = coCov;
requestedCovariates.add(cyCov); requestedCovariates[3] = cyCov;
ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates); ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates);

11
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationReportUnitTest.java
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@ -37,7 +37,6 @@ public class RecalibrationReportUnitTest {
quantizationInfo.noQuantization(); quantizationInfo.noQuantization();
final List<Covariate> requiredCovariates = new LinkedList<Covariate>(); final List<Covariate> requiredCovariates = new LinkedList<Covariate>();
final List<Covariate> optionalCovariates = new LinkedList<Covariate>(); final List<Covariate> optionalCovariates = new LinkedList<Covariate>();
final List<Covariate> requestedCovariates = new LinkedList<Covariate>();
final ReadGroupCovariate rgCovariate = new ReadGroupCovariate(); final ReadGroupCovariate rgCovariate = new ReadGroupCovariate();
rgCovariate.initialize(RAC); rgCovariate.initialize(RAC);
@ -60,10 +59,12 @@ public class RecalibrationReportUnitTest {
BQSRKeyManager cvKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates); BQSRKeyManager cvKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
keysAndTablesMap.put(cvKeyManager, new HashMap<Long, RecalDatum>()); keysAndTablesMap.put(cvKeyManager, new HashMap<Long, RecalDatum>());
for (Covariate cov : requiredCovariates) final Covariate[] requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()];
requestedCovariates.add(cov); int covariateIndex = 0;
for (Covariate cov : optionalCovariates) for (final Covariate cov : requiredCovariates)
requestedCovariates.add(cov); requestedCovariates[covariateIndex++] = cov;
for (final Covariate cov : optionalCovariates)
requestedCovariates[covariateIndex++] = cov;
final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("id"); final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("id");
rg.setPlatform("illumina"); rg.setPlatform("illumina");

13
public/java/test/org/broadinstitute/sting/utils/recalibration/BaseRecalibrationUnitTest.java
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@ -48,7 +48,6 @@ public class BaseRecalibrationUnitTest {
RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
List<Covariate> requiredCovariates = new ArrayList<Covariate>(); List<Covariate> requiredCovariates = new ArrayList<Covariate>();
List<Covariate> optionalCovariates = new ArrayList<Covariate>(); List<Covariate> optionalCovariates = new ArrayList<Covariate>();
ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>();
dataManager = new org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager(true, 4); dataManager = new org.broadinstitute.sting.gatk.walkers.recalibration.RecalDataManager(true, 4);
keysAndTablesMap = new LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>>(); keysAndTablesMap = new LinkedHashMap<BQSRKeyManager, Map<Long, RecalDatum>>();
@ -74,10 +73,12 @@ public class BaseRecalibrationUnitTest {
BQSRKeyManager cvKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates); BQSRKeyManager cvKeyManager = new BQSRKeyManager(requiredCovariates, optionalCovariates);
keysAndTablesMap.put(cvKeyManager, new HashMap<Long, RecalDatum>()); keysAndTablesMap.put(cvKeyManager, new HashMap<Long, RecalDatum>());
for (Covariate cov : requiredCovariates) final Covariate[] requestedCovariates = new Covariate[requiredCovariates.size() + optionalCovariates.size()];
requestedCovariates.add(cov); int covariateIndex = 0;
for (Covariate cov : optionalCovariates) for (final Covariate cov : requiredCovariates)
requestedCovariates.add(cov); requestedCovariates[covariateIndex++] = cov;
for (final Covariate cov : optionalCovariates)
requestedCovariates[covariateIndex++] = cov;
readCovariates = RecalDataManager.computeCovariates(read, requestedCovariates); readCovariates = RecalDataManager.computeCovariates(read, requestedCovariates);
@ -112,7 +113,7 @@ public class BaseRecalibrationUnitTest {
} }
QuantizationInfo quantizationInfo = new QuantizationInfo(quantizedQuals, qualCounts); QuantizationInfo quantizationInfo = new QuantizationInfo(quantizedQuals, qualCounts);
quantizationInfo.noQuantization(); quantizationInfo.noQuantization();
baseRecalibration = new BaseRecalibration(quantizationInfo, keysAndTablesMap, requestedCovariates.toArray()); baseRecalibration = new BaseRecalibration(quantizationInfo, keysAndTablesMap, requestedCovariates);
} }